Literature DB >> 24938631

The emergence of proteome-wide technologies: systematic analysis of proteins comes of age.

Michal Breker1, Maya Schuldiner1.   

Abstract

During the lifetime of a cell proteins can change their localization, alter their abundance and undergo modifications, all of which cannot be assayed by tracking mRNAs alone. Methods to study proteomes directly are coming of age, thereby opening new perspectives on the role of post-translational regulation in stabilizing the cellular milieu. Proteomics has undergone a revolution, and novel technologies for the systematic analysis of proteins have emerged. These methods can expand our ability to acquire information from single proteins to proteomes, from static to dynamic measures and from the population level to the level of single cells. Such approaches promise that proteomes will soon be studied at a similar level of dynamic resolution as has been the norm for transcriptomes.

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Year:  2014        PMID: 24938631     DOI: 10.1038/nrm3821

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  149 in total

1.  Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.

Authors:  Alex Sigal; Ron Milo; Ariel Cohen; Naama Geva-Zatorsky; Yael Klein; Inbal Alaluf; Naamah Swerdlin; Natalie Perzov; Tamar Danon; Yuvalal Liron; Tal Raveh; Anne E Carpenter; Galit Lahav; Uri Alon
Journal:  Nat Methods       Date:  2006-07       Impact factor: 28.547

2.  Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays.

Authors:  Yifat Merbl; Marc W Kirschner
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-30       Impact factor: 11.205

3.  Monitoring protein-protein interactions between the mammalian integral membrane transporters and PDZ-interacting partners using a modified split-ubiquitin membrane yeast two-hybrid system.

Authors:  Serge M Gisler; Saranya Kittanakom; Daniel Fuster; Victoria Wong; Mia Bertic; Tamara Radanovic; Randy A Hall; Heini Murer; Jürg Biber; Daniel Markovich; Orson W Moe; Igor Stagljar
Journal:  Mol Cell Proteomics       Date:  2008-04-11       Impact factor: 5.911

Review 4.  Proteome dynamics: revisiting turnover with a global perspective.

Authors:  Amy J Claydon; Robert Beynon
Journal:  Mol Cell Proteomics       Date:  2012-11-02       Impact factor: 5.911

5.  Proteomic and phosphoproteomic comparison of human ES and iPS cells.

Authors:  Douglas H Phanstiel; Justin Brumbaugh; Craig D Wenger; Shulan Tian; Mitchell D Probasco; Derek J Bailey; Danielle L Swaney; Mark A Tervo; Jennifer M Bolin; Victor Ruotti; Ron Stewart; James A Thomson; Joshua J Coon
Journal:  Nat Methods       Date:  2011-09-11       Impact factor: 28.547

6.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

7.  The quantitative proteome of a human cell line.

Authors:  Martin Beck; Alexander Schmidt; Johan Malmstroem; Manfred Claassen; Alessandro Ori; Anna Szymborska; Franz Herzog; Oliver Rinner; Jan Ellenberg; Ruedi Aebersold
Journal:  Mol Syst Biol       Date:  2011-11-08       Impact factor: 11.429

8.  Towards lipidomics of low-abundant species for exploring tumor heterogeneity guided by high-resolution mass spectrometry imaging.

Authors:  Jonathan Cimino; David Calligaris; Johann Far; Delphine Debois; Silvia Blacher; Nor Eddine Sounni; Agnès Noel; Edwin De Pauw
Journal:  Int J Mol Sci       Date:  2013-12-17       Impact factor: 5.923

9.  Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

Authors:  Louis-François Handfield; Yolanda T Chong; Jibril Simmons; Brenda J Andrews; Alan M Moses
Journal:  PLoS Comput Biol       Date:  2013-06-13       Impact factor: 4.475

Review 10.  Protein-protein interaction detection: methods and analysis.

Authors:  V Srinivasa Rao; K Srinivas; G N Sujini; G N Sunand Kumar
Journal:  Int J Proteomics       Date:  2014-02-17
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  28 in total

Review 1.  Proteomic contributions to our understanding of vaccine and immune responses.

Authors:  Allison C Galassie; Andrew J Link
Journal:  Proteomics Clin Appl       Date:  2015-09-10       Impact factor: 3.494

Review 2.  Multidimensional proteomics for cell biology.

Authors:  Mark Larance; Angus I Lamond
Journal:  Nat Rev Mol Cell Biol       Date:  2015-04-10       Impact factor: 94.444

Review 3.  Spatial proteomics: a powerful discovery tool for cell biology.

Authors:  Emma Lundberg; Georg H H Borner
Journal:  Nat Rev Mol Cell Biol       Date:  2019-05       Impact factor: 94.444

4.  A scalable strategy for high-throughput GFP tagging of endogenous human proteins.

Authors:  Manuel D Leonetti; Sayaka Sekine; Daichi Kamiyama; Jonathan S Weissman; Bo Huang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-06       Impact factor: 11.205

5.  Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples.

Authors:  Zhengwei Chen; Junfeng Huang; Lingjun Li
Journal:  Trends Analyt Chem       Date:  2018-10-15       Impact factor: 12.296

6.  An Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes.

Authors:  Wenxuan Cai; Jianhua Zhang; Willem J de Lange; Zachery R Gregorich; Hannah Karp; Emily T Farrell; Stanford D Mitchell; Trisha Tucholski; Ziqing Lin; Mitch Biermann; Sean J McIlwain; J Carter Ralphe; Timothy J Kamp; Ying Ge
Journal:  Circ Res       Date:  2019-10-01       Impact factor: 17.367

7.  Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems.

Authors:  Duygu Dikicioglu
Journal:  Methods Mol Biol       Date:  2019

Review 8.  Integrating -Omics Approaches into Human Population-Based Studies of Prenatal and Early-Life Exposures.

Authors:  Todd M Everson; Carmen J Marsit
Journal:  Curr Environ Health Rep       Date:  2018-09

Review 9.  System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders.

Authors:  Fernando Gomez-Pinilla; Xia Yang
Journal:  Prog Neurobiol       Date:  2018-07-27       Impact factor: 11.685

10.  Proteomic studies of bone and skeletal health outcomes.

Authors:  Carrie M Nielson; Jon M Jacobs; Eric S Orwoll
Journal:  Bone       Date:  2019-04-04       Impact factor: 4.398

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